Moselio Schaechter

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January 17, 2013

Teaching Students To See Through “Microbial Eyes"

by Mark O. Martin

The voyage of discovery is not in seeking new landscapes but in having new eyes. - Marcel Proust

At my primarily undergraduate institution (3,000 students total, 12 Biology faculty, over 50 Biology majors graduated per year), there is only one microbiology course, and it is generally taught to seniors (and not all seniors at that).  Considering the power and primacy of the microbial world, I have always found that lack of coverage pedagogically unsettling.  No biology major could graduate without learning a fair amount about plants; what about bacteria and archaea?  It is certainly true that some classes—cell biology, genetics, and molecular biology come to mind—have aspects that intersect with matters microbial.  But I find that my seniors, after a semester of my prokaryotic proselytizing, are very aware of a significant gap in their education.

“Doc Martin’s” 2012 Microbiology class.

This is why I would urge any and all microbiologists out there to push for more microbiology, earlier in the curriculum, both in lecture and laboratory.  I do what I can to promote “microbial pride” among my seniors, as you can see from the photograph of my class this semester.  I even came up with a logo, which I showed during a presentation at the American Society for Microbiology General Meeting in San Francisco last June, suggesting that we microbiologists should push to “occupy the curriculum,” intellectually speaking. After all, consider how genetics, molecular biology, and biochemistry have progressed over the past century.  Now consider the path of that progress without the use of prokaryotes as a model system!  I believe we will also find that the fields of ecology and evolution will also be equally as indebted to bacteria and archaea over time.

I felt it ought to be included in the freshman sequence we teach here at the University of Puget Sound.  One semester is called “The Unity of Life,” and is an introduction to cell and molecular biology; the other semester is called “The Diversity of Life,” and focuses on ecology, groups of living things, and evolutionary topics.   Here is what some of my students wrote in response to my question:


  • I had never heard of biofilms before this class, yet they are common in nature (even involved in many human diseases)—this could fit into either semester in the first year.
  • First year students should learn that Rubisco is a prokaryotic enzyme, not just found in plants (and that chloroplasts are enslaved cyanobacteria!).  Also, that nitrogenase is prokaryotic, and what would happen if it stopped working.
  • Why not present bacterial and archaean compartments when discussing eukaryotic compartmentalization (Golgi, ER, etc)?  Bacteria aren’t “bags of enzymes.”
  • Freshmen REALLY need to hear more about the archaea—both in class and in lab.  They are not just extremophiles, either!
  • Diversity of Life could include more microbial symbioses:  leafcutter ants and Pseudonorcardia, or weird Wolbachia, or Buchnera.  Maybe even a lab using PCR to search for Wolbachia in insects?
  • I thought learning about antibiotics was really important to everyday life, and I’ll bet freshmen would feel the same way.
  • Presenting a simple quorum sensing model could help freshmen see how cell-cell signaling works as a concept.  It could prepare them for learning about more complicated eukaryotic cell-cell signaling in upper division courses, and getting them thinking about microbial communication early on.  Could our QS lab exercise be adapted to the freshman class?
  • Students should be hearing more about the prokaryotic role in elemental cycling .  I really didn’t know how important prokaryotes were to those cycles.
  • Could professors in our classes please quit calling bacteria “simple”?  Also, could they stop telling us that bacteria don’t have cytoskeletons (because they do), and lack compartmentalization (because they have compartments)?
  • Freshmen could hear more about the Tree of Life and how it came to be.
  • I think that first year students could discuss the controversy over the term “prokaryote,” and learn a lot about microbiology by doing so.

To the above, I would simply add what Walt Whitman wrote many years ago:  “We convince by our presence.”  My students become “true believers” in microbial supremacy because I show them the centrality of the microbial world to almost every aspect of biology.  We microbiologists do need to continue to preach our microbial gospel to freshmen!

Inspired by this, I am going to introduce some additional microbially oriented topics in my “The Unity of Life” course next semester:  biofilms, antibiotics, quorum sensing, microbial interactions, and a new investigative laboratory exercise involving biofilms.  Wish me luck at “occupying the curriculum.”  Change can be challenging, in pedagogy as everywhere else.  Still, I must try, because in the biosphere, our microbial relatives are far, far more than merely the “99%”!


Mark O. Martin is an avowed “microbial supremacist” as well as an Associate Professor of Biology at the University of Puget Sound in Tacoma, Washington. He is a frequent contributor to STC and was an Associate Blogger for several years.

Editor's Note: Mark puts his money where his mouth is and teaches what must be a dream undergraduate micro course (as judged by the students' ratings). As an example, see the "nanobiographies" that his students wrote as a class assignment.


Very well said Mark, I teach Microbiology too and I feel just as strongly. Your work is inspiring me to do some similar assignment with the students. Thanks!!

Great job Mark! As you know, I'm the "biggest fan" of microbiology educators at ASM. I'll add that ASM stands ready to help educators Occupy the Curriculum! Over the past year and a half, the ASM community of educators worked hard to create the "Recommended Curriculum Guidelines for Undergraduate Microbiology." Everyone can read about this document and the consensus-building process that created it in the Journal of Microbiology & Biology Education here: The guidelines are based on the AAAS/NSF "Vision and Change in Undergraduate Biology Education: A Call to Action" report ( This year, at the ASM Conference for Undergraduate Educators (, faculty attendees will begin working on a list of learning objectives that align with the recommended curriculum guidelines with the long-term goal of building a scaffold of lab/classroom activities that scaffold with these objectives. Go microbes & thank you to Mark and all the other faculty members who are helping to raise the next generation of scientists!

Very true.

We need many more microbiologists for the revolutionary road ahead.


I'm delighted to hear your voice again on STC, once again reminding us that we still have a long way to go before the microbes receive the attention they warrant in university biology departments. Keep up your good work on their behalf!

Thanks for the great ideas and literature references Mark, Elio, et al.

Mark, I agree that educators probably have a bigger impact than they suspect--please, briefly, let me explain.

These emerging platforms we are using now--e.g. blogs, podcasts, and open access journals--are at the very core of my personal microbiological education. I started my biology career working seasonal jobs counting fish in rural areas with the dept. of fish and wildlife here in Oregon. Tired of seasonal work, and through a possible inflation of my scientific skills, I landed a job as an old school (manual) QC lab technician at a small diagnostics company that makes specialized microbial casseroles(agar mediums,etc.)for vets and medical labs.

Your horizontal transfer of information pertaining to the elegant truths and exquisite inter-relationships of nature through the lens of microbial life has certainly occupied my curriculum and I now consider myself somewhat of a provincial and humble novice microbiologist. Thanks again all,

Thanks to you all! Elisa, your comment reminds everyone just how important elementary and secondary school science can be! I had a wonderful science teacher in junior high school who influenced me greatly. Ditto my college professors, in particular Syd Rittenberg (who taught my intro microbiology course) and Bob Romig. Sometimes, educators have a bigger impact than they suspect...

Gemma, that is very kind of you. I'm trying to push more micro into our first year curriculum, and several faculty colleagues are supporting me in this. We'll see how it goes...

Barry, "Lives of a Cell" got me thinking about microbiology early on, as well. DItto Betsey Dyer's great book! I would also recommend "March of the Microbes" by the wonderful John Ingraham.

Finally, can I tip my hat to the creator of much of my microbial artwork, the talented Kaitlin Reiss ( who has a deep love of nature (even the teeny bits!) and a quirky, delightful sense of humor.

Also, thanks for the kind words about my class, Elio.

I love this and luckily when I was in high school my AP Biology teacher was a Microbiologist. She instilled a love of microbiology within me and I am a senior now at Weber State University in Microbiology. Truly the best decision I have ever made.

Great article and ideas, Mark. My major is in Biological Sciences and I had a mandatory, two-semester long Micro course as a sophomore. That course shaped and nurtured my interests early on and had a tremendous influence in my learning process and in becoming a microbiologist. The earliest exposure to microbiology, the better biological background for the students. And finally,... That's it! I am taking a sabbatical so I can audit your course ;o)

i guess i lucked out in high school by subscribing to natural history mag and thus at the end of the year got a copy of Lewis Thomas' "lives of a cell" and thus got turned onto Lynn Margulis early on. this was in the 70s.

i wish i had had the opportunity to discover something like Betsey Dexter Dyer's "A Field Guide to Bacteria" back then too!">">

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